Workflows

These workflows are associated with Assembly of metagenomic sequencing data

To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.

flowchart TD
  0["ℹ️ Input Collection\nInput Dataset Collection"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["metaSPAdes"];
  0 -->|output| 1;
  833d79ff-e16f-414c-9c41-db8dbfa8ed6b["Output\nmetaSPAdes on input dataset(s): Scaffolds"];
  1 --> 833d79ff-e16f-414c-9c41-db8dbfa8ed6b;
  style 833d79ff-e16f-414c-9c41-db8dbfa8ed6b stroke:#2c3143,stroke-width:4px;
  10319152-d2f9-47d8-be41-f956a57e86d3["Output\nmetaSPAdes on input dataset(s): Assembly graph"];
  1 --> 10319152-d2f9-47d8-be41-f956a57e86d3;
  style 10319152-d2f9-47d8-be41-f956a57e86d3 stroke:#2c3143,stroke-width:4px;
  b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633["Output\nmetaSPAdes on input dataset(s): Assembly graph with scaffolds"];
  1 --> b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633;
  style b1ffc3a4-8e39-4255-ac57-fd7cfb9c1633 stroke:#2c3143,stroke-width:4px;
  b6b74c9d-5a16-4725-a1d1-11c1f05ee909["Output\nmetaSPAdes on input dataset(s): Contigs"];
  1 --> b6b74c9d-5a16-4725-a1d1-11c1f05ee909;
  style b6b74c9d-5a16-4725-a1d1-11c1f05ee909 stroke:#2c3143,stroke-width:4px;
  2["MEGAHIT"];
  0 -->|output| 2;
  3["Bowtie2"];
  0 -->|output| 3;
  2 -->|output| 3;
  4["megahit contig2fastg"];
  2 -->|output| 4;
  5["Quast"];
  2 -->|output| 5;
  0 -->|output| 5;
  6["Bandage Image"];
  4 -->|fastg| 6;
  7["Bandage Info"];
  4 -->|fastg| 7;
  8["Column join"];
  7 -->|outfile| 8;
	

flowchart TD
  0["ℹ️ Input Dataset\nERR2231567_1.fastq.gz"];
  style 0 stroke:#2c3143,stroke-width:4px;
  1["ℹ️ Input Dataset\nERR2231567_2.fastq.gz"];
  style 1 stroke:#2c3143,stroke-width:4px;
  2["Cutadapt"];
  0 -->|output| 2;
  1 -->|output| 2;
  3["MEGAHIT"];
  2 -->|out1| 3;
  2 -->|out2| 3;
  4["Bowtie2"];
  2 -->|out1| 4;
  2 -->|out2| 4;
  3 -->|output| 4;
  5["BAM filter"];
  4 -->|output| 5;
  6["BAM filter"];
  4 -->|output| 6;
  7["Convert, Merge, Randomize"];
  5 -->|outfile| 7;
  8["Convert, Merge, Randomize"];
  6 -->|outfile| 8;
  9["Select random lines"];
  7 -->|out_file1| 9;
  10["Select random lines"];
  8 -->|out_file1| 10;
  11["Filter Tabular"];
  9 -->|out_file1| 11;
  12["Filter Tabular"];
  10 -->|out_file1| 12;
  13["Unique"];
  11 -->|output| 13;
  14["Unique"];
  12 -->|output| 14;
  15["Concatenate datasets"];
  13 -->|outfile| 15;
  14 -->|outfile| 15;
  16["seqtk_subseq"];
  2 -->|out1| 16;
  15 -->|out_file1| 16;
  17["seqtk_subseq"];
  2 -->|out2| 17;
  15 -->|out_file1| 17;
  18["FastQC"];
  16 -->|default| 18;
  19["FastQC"];
  17 -->|default| 19;
	

Importing into Galaxy

Hands-on: Importing a workflow

• Click on Workflow on the top menu bar of Galaxy. You will see a list of all your workflows.
• Click on galaxy-upload Import at the top-right of the screen
• Provide your workflow
  • Option 1: Paste the URL of the workflow into the box labelled “Archived Workflow URL”
  • Option 2: Upload the workflow file in the box labelled “Archived Workflow File”
• Click the Import workflow button

Below is a short video demonstrating how to import a workflow from GitHub using this procedure: